Fix updateAPI client generation and update API clients (#4829)

env/custom.sh

@@ -1,2 +0,0 @@
-#export CBIOPORTAL_URL="http://localhost:8081"
-#export GENOME_NEXUS_URL="https://www.genomenexus.org"

package.json

@@ -31,8 +31,8 @@
     "heroku-postbuild": "yarn run build && yarn add [email protected] -g",
     "updateAPI": "yarn run fetchAPI && yarn run buildAPI && yarn run updateOncoKbAPI && yarn run updateGenomeNexusAPI",
     "convertToSwagger2": "./scripts/convert_to_swagger2.sh && yarn run extendSwagger2Converter",
-    "fetchAPILocal": "export CBIOPORTAL_URL=http://localhost:8090 && curl -s -L -k ${CBIOPORTAL_URL}/v3/api-docs/public | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -s -L -k ${CBIOPORTAL_URL}/v3/api-docs/internal | json | grep -v host | grep -v basePath | grep -v termsOfService > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json",
-    "fetchAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -s -L -k ${CBIOPORTAL_URL}/v3/api-docs/public  > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -s -L -k ${CBIOPORTAL_URL}/v3/api-docs/internal | json  > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json && yarn run convertToSwagger2",
+    "fetchAPILocal": "export CBIOPORTAL_URL=http://localhost:8090 && curl -s -L -k ${CBIOPORTAL_URL}/api/v3/api-docs/public | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -s -L -k ${CBIOPORTAL_URL}/api/v3/api-docs/internal | json | grep -v host | grep -v basePath | grep -v termsOfService > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json",
+    "fetchAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -s -L -k ${CBIOPORTAL_URL}/api/v3/api-docs/public  > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -s -L -k ${CBIOPORTAL_URL}/api/v3/api-docs/internal | json  > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json && yarn run convertToSwagger2",
     "extendSwagger2Converter": "node scripts/extend_converter.js packages/cbioportal-ts-api-client/src/generated CBioPortalAPI CBioPortalAPIInternal",
     "buildAPI": "node scripts/generate-api.js packages/cbioportal-ts-api-client/src/generated CBioPortalAPI CBioPortalAPIInternal",
     "updateOncoKbAPI": "yarn run fetchOncoKbAPI && yarn run buildOncoKbAPI",
@@ -42,7 +42,8 @@
     "fetchG2SAPI": "curl -s -k http://g2s.genomenexus.org/v2/api-docs?group=api > packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI-docs.json",
     "buildG2SAPI": "node scripts/generate-api.js packages/genome-nexus-ts-api-client/src/generated Genome2StructureAPI",
     "updateGenomeNexusAPI": "yarn run fetchGenomeNexusAPI && yarn run buildGenomeNexusAPI",
-    "fetchGenomeNexusAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -s -k ${GENOME_NEXUS_URL}/v2/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json && curl -s -k ${GENOME_NEXUS_URL}/v2/api-docs?group=internal | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json",
+    "fetchGenomeNexusAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -s -L -k ${GENOME_NEXUS_URL}/v2/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json && curl -s -L -k ${GENOME_NEXUS_URL}/v2/api-docs?group=internal | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json",
+
     "buildGenomeNexusAPI": "node scripts/generate-api.js packages/genome-nexus-ts-api-client/src/generated GenomeNexusAPI GenomeNexusAPIInternal",
     "updateHotspotGenes": "./scripts/get_hotspot_genes.sh > src/shared/static-data/hotspotGenes.json",
     "compileOqlParser": "cd src/shared/lib/oql && pegjs oql-parser.pegjs",

packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json

@@ -69,7 +69,7 @@
         ],
         "parameters": [
           {
-            "description": "Secret API key passed in HTTP header. The key is configured in portal.properties of the portal instance.",
+            "description": "Secret API key passed in HTTP header. The key is configured in application.properties of the portal instance.",
             "in": "header",
             "name": "X-API-KEY",
             "required": true,

packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts

@@ -1348,7 +1348,7 @@ export default class CBioPortalAPIInternal {
      * Clear and reinitialize caches
      * @method
      * @name CBioPortalAPIInternal#clearAllCachesUsingDELETE
-     * @param {string} xApiKey - Secret API key passed in HTTP header. The key is configured in portal.properties of the portal instance.
+     * @param {string} xApiKey - Secret API key passed in HTTP header. The key is configured in application.properties of the portal instance.
      * @param {boolean} springManagedCache - Clear Spring-managed caches
      */
     clearAllCachesUsingDELETEWithHttpInfo(parameters: {
@@ -1397,7 +1397,7 @@ export default class CBioPortalAPIInternal {
      * Clear and reinitialize caches
      * @method
      * @name CBioPortalAPIInternal#clearAllCachesUsingDELETE
-     * @param {string} xApiKey - Secret API key passed in HTTP header. The key is configured in portal.properties of the portal instance.
+     * @param {string} xApiKey - Secret API key passed in HTTP header. The key is configured in application.properties of the portal instance.
      * @param {boolean} springManagedCache - Clear Spring-managed caches
      */
     clearAllCachesUsingDELETE(parameters: {

packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json

@@ -1594,15 +1594,6 @@
         },
         "ncitCode": {
           "type": "string"
-        },
-        "synonyms": {
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "uuid": {
-          "type": "string"
         }
       }
     },

packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts

@@ -186,10 +186,6 @@ export type Drug = {
 
         'ncitCode': string
 
-        'synonyms': Array < string >
-
-        'uuid': string
-
 };
 export type EnsemblFilter = {
     'geneIds': Array < string >